PDB assembly (biological unit, BU)ID + hyphen + assembly-ID (e.g.1oel-1)Or click the image of AU/BU, which will be shown below when you input an PDB-ID

SASBDB modelSASBDB-ID or model-ID (e.g.SASDAA5, 100, sas-100)

Comparison of 3 databanks

Samples:

Structure data giving symbolic results

This is an EM map data of the RNA polymerase II at 25 A resolution. You will find atomic models and EM maps of RNA polymerase structures from the EMDB & PDB. Perform search.

The DNA clamp is a ring shaped oligomer essential for DNA metabolism. All the DNA clamps have similar shapes, while bacterial clamps are dimer ring, and archaeal/eukaryal ones are trimer ring. By search using this trimer clamp, you will find dimer clamp structures as well. Perform search.

EF-Tu/tRNA complex (RNA + protein) and EF-G (monomeric protein) have similar shapes despite their different compositions ("molecular mimicry"). You will find both EFs by this search. Perform search.

This is a dummy-atom model of lumazine synthase obtained by SAS. You will find many crystal structures of same molecules. Perform search.

Many 70S ribosome structure data are stored in EMDB and PDB. Omokage search is useful to find out such the huge molecule structures. Perform search.

For huger molecule, such as this rice dwarf virus, Omokage search can be used. Perform search.

Not only for the huge structures but also for small molecules, such as this DNA fragment, this tool might be useful. By this search, some proteins having similar shape to this DNA fragment are found (for good or for bad). Perform search.

This is another example for small molecules. Which proteins have simialar shapes to this beta-propeller structure? Perform search.

EMDB

PDB

SASBDB

You can use your original data or a modified data for the search. Select type of the file and upload the file by this form.

3D density map file in CCP4/MRC format (voxels must be cubic)Max voxel number is ~200. Large map data should be trimmed and shrined before uploading.Uncompressed or gzip-compressed file is uploadable

File: Surface level:

Codebook vectors made by qvol or qpdb tool in Situs package. Two models, model with 30 and 50 points are required for Omokage comparison.

30-dot model: 50-dot model:

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About Omokage search

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News

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Jul 12, 2017. Major update of PDB

Major update of PDB

wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.

In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.